bims-meprid Biomed News
on Metabolic-dependent epigenetic reprogramming in differentiation and disease
Issue of 2021–03–07
fourteen papers selected by
Alessandro Carrer, Veneto Institute of Molecular Medicine
  1. Mitochondria as Signaling Organelles Control Mammalian Stem Cell Fate.
  2. Malonate Promotes Adult Cardiomyocyte Proliferation and Heart Regeneration.
  3. Epigenomic links from metabolism-methionine and chromatin architecture.
  4. Itaconate Alters Succinate and Coenzyme A Metabolism via Inhibition of Mitochondrial Complex II and Methylmalonyl-CoA Mutase.
  5. Author Correction: BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8+ T cells.
  6. Butyrate Shapes Immune Cell Fate and Function in Allergic Asthma.
  7. Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation.
  8. Microbial Regulation of Host Physiology by Short-chain Fatty Acids.
  9. Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells.
  10. Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
  11. PSPH promotes melanoma growth and metastasis by metabolic deregulation-mediated transcriptional activation of NR4A1.
  12. How Does Protein Nutrition Affect the Epigenetic Changes in Pig? A Review.
  13. Immunoprecipitation of Acetyl-lysine And Western Blotting of Long-chain acyl-CoA Dehydrogenases and Beta-hydroxyacyl-CoA Dehydrogenase in Palmitic Acid Treated Human Renal Tubular Epithelial Cells.
  14. Lysine crotonylation is widespread on proteins of diverse functions and localizations in Toxoplasma gondii.
  1. Cell Stem Cell. 2021 Mar 04. pii: S1934-5909(21)00061-8. [Epub ahead of print]28(3): 394-408
    Mitochondria as Signaling Organelles Control Mammalian Stem Cell Fate.
    Ram Prosad Chakrabarty, Navdeep S Chandel.
      Recent evidence supports the notion that mitochondrial metabolism is necessary for the determination of stem cell fate. Historically, mitochondrial metabolism is linked to the production of ATP and tricarboxylic acid (TCA) cycle metabolites to support stem cell survival and growth, respectively. However, it is now clear that beyond these canonical roles, mitochondria as signaling organelles dictate stem cell fate and function. In this review, we focus on key conceptual ideas on how mitochondria control mammalian stem cell fate and function through reactive oxygen species (ROS) generation, TCA cycle metabolite production, NAD+/NADH ratio regulation, pyruvate metabolism, and mitochondrial dynamics.
    Keywords:  L-2-HG; ROS; TCA cycle; acetyl-CoA; epigenetics; mitochondrial dynamics; pyruvate
    DOI:  https://doi.org/10.1016/j.stem.2021.02.011
  2. Circulation. 2021 Mar 05.
    Malonate Promotes Adult Cardiomyocyte Proliferation and Heart Regeneration.
    Jiyoung Bae, Rebecca J Salamon, Emma B Brandt, Wyatt G Paltzer, Ziheng Zhang, Emily C Britt, Timothy A Hacker, Jing Fan, Ahmed I Mahmoud.
      Background: Neonatal mouse cardiomyocytes undergo a metabolic switch from glycolysis to oxidative phosphorylation, which results in a significant increase in reactive oxygen species (ROS) production that induces DNA damage. These cellular changes contribute to cardiomyocyte cell cycle exit and loss of the capacity for cardiac regeneration. The mechanisms that regulate this metabolic switch and the increase in ROS production have been relatively unexplored. Current evidence suggests that elevated ROS production in ischemic tissues occurs due to accumulation of the mitochondrial metabolite succinate during ischemia via succinate dehydrogenase (SDH), and this succinate is rapidly oxidized at reperfusion. Interestingly, mutations in SDH in familial cancer syndromes have been demonstrated to promote a metabolic shift into glycolytic metabolism, suggesting a potential role for SDH in regulating cellular metabolism. Whether succinate and SDH regulate cardiomyocyte cell cycle activity and the cardiac metabolic state remains unclear. Methods: Here, we investigated the role of succinate and succinate dehydrogenase (SDH) inhibition in regulation of postnatal cardiomyocyte cell cycle activity and heart regeneration. Results: Our results demonstrate that injection of succinate in neonatal mice results in inhibition of cardiomyocyte proliferation and regeneration. Our evidence also shows that inhibition of SDH by malonate treatment after birth extends the window of cardiomyocyte proliferation and regeneration in juvenile mice. Remarkably, extending malonate treatment to the adult mouse heart following myocardial infarction injury results in a robust regenerative response within 4 weeks following injury via promoting adult cardiomyocyte proliferation and revascularization. Our metabolite analysis following SDH inhibition by malonate induces dynamic changes in adult cardiac metabolism. Conclusions: Inhibition of SDH by malonate promotes adult cardiomyocyte proliferation, revascularization, and heart regeneration via metabolic reprogramming. These findings support a potentially important new therapeutic approach for human heart failure.
    Keywords:  heart regeneration; succinate dehydrogenase
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.120.049952
  3. Curr Opin Chem Biol. 2021 Mar 02. pii: S1367-5931(21)00014-4. [Epub ahead of print]63 11-18
    Epigenomic links from metabolism-methionine and chromatin architecture.
    Zhengtao Xiao, Jason W Locasale.
      Chromatin and associated epigenetic marks provide important platforms for gene regulation in response to metabolic changes associated with environmental exposures, including physiological stress, nutritional deprivation, and starvation. Numerous studies have shown that fluctuations of key metabolites can influence chromatin modifications, but their effects on chromatin structure (e.g. chromatin compaction, nucleosome arrangement, and chromatin loops) and how they appropriately deposit specific chemical modification on chromatin are largely unknown. Here, focusing on methionine metabolism, we discuss recent developments of metabolic effects on chromatin modifications and structure, as well as consequences on gene regulation.
    Keywords:  Chromatin; Epigenetics; Metabolism; Methionine; Transcription
    DOI:  https://doi.org/10.1016/j.cbpa.2021.01.011
  4. Metabolites. 2021 Feb 18. pii: 117. [Epub ahead of print]11(2):
    Itaconate Alters Succinate and Coenzyme A Metabolism via Inhibition of Mitochondrial Complex II and Methylmalonyl-CoA Mutase.
    Thekla Cordes, Christian M Metallo.
      Itaconate is a small molecule metabolite that is endogenously produced by cis-aconitate decarboxylase-1 (ACOD1) in mammalian cells and influences numerous cellular processes. The metabolic consequences of itaconate in cells are diverse and contribute to its regulatory function. Here, we have applied isotope tracing and mass spectrometry approaches to explore how itaconate impacts various metabolic pathways in cultured cells. Itaconate is a competitive and reversible inhibitor of Complex II/succinate dehydrogenase (SDH) that alters tricarboxylic acid (TCA) cycle metabolism leading to succinate accumulation. Upon activation with coenzyme A (CoA), itaconyl-CoA inhibits adenosylcobalamin-mediated methylmalonyl-CoA (MUT) activity and, thus, indirectly impacts branched-chain amino acid (BCAA) metabolism and fatty acid diversity. Itaconate, therefore, alters the balance of CoA species in mitochondria through its impacts on TCA, amino acid, vitamin B12, and CoA metabolism. Our results highlight the diverse metabolic pathways regulated by itaconate and provide a roadmap to link these metabolites to potential downstream biological functions.
    Keywords:  TCA cycle metabolism; acetyl-CoA; branched-chain amino acids (BCAA); isotopic tracing; itaconate; itaconyl-CoA; methylmalonate; odd-chain fatty acids (OCFAs); propionyl-CoA; succinate; succinate dehydrogenase; vitamin B12
    DOI:  https://doi.org/10.3390/metabo11020117
  5. Nat Immunol. 2021 Mar 03.
    Author Correction: BACH2 enforces the transcriptional and epigenetic programs of stem-like CD8+ T cells.
    Chen Yao, Guohua Lou, Hong-Wei Sun, Ziang Zhu, Yi Sun, Zeyu Chen, Daniel Chauss, E Ashley Moseman, Jun Cheng, Marc A D'Antonio, Wangke Shi, Junwei Shi, Kohei Kometani, Tomohiro Kurosaki, E John Wherry, Behdad Afzali, Luca Gattinoni, Yuwen Zhu, Dorian B McGavern, John J O'Shea, Pamela L Schwartzberg, Tuoqi Wu.
      
    DOI:  https://doi.org/10.1038/s41590-021-00906-4
  6. Front Immunol. 2021 ;12 628453
    Butyrate Shapes Immune Cell Fate and Function in Allergic Asthma.
    William Yip, Michael R Hughes, Yicong Li, Alissa Cait, Martin Hirst, William W Mohn, Kelly M McNagny.
      The microbiome plays a fundamental role in how the immune system develops and how inflammatory responses are shaped and regulated. The "gut-lung axis" is a relatively new term that highlights a crucial biological crosstalk between the intestinal microbiome and lung. A growing body of literature suggests that dysbiosis, perturbation of the gut microbiome, is a driving force behind the development, and severity of allergic asthma. Animal models have given researchers new insights into how gut microbe-derived components and metabolites, such as short-chain fatty acids (SCFAs), influence the development of asthma. While the full understanding of how SCFAs influence allergic airway disease remains obscure, a recurring theme of epigenetic regulation of gene expression in several immune cell compartments is emerging. This review will address our current understanding of how SCFAs, and specifically butyrate, orchestrates cell behavior, and epigenetic changes and will provide a detailed overview of the effects of these modifications on immune cells in the context of allergic airway disease.
    Keywords:  HDAC inhibitor (histone deacetylase inhibitor); SCFA (short chain fatty acids); allergic asthma; butyrate; cell fate and differentiation; epigenetics; inflammation; microbiome
    DOI:  https://doi.org/10.3389/fimmu.2021.628453
  7. Mol Cell. 2021 Feb 23. pii: S1097-2765(21)00095-2. [Epub ahead of print]
    Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation.
    Wei Tan, Pei Jiang, Wanjun Zhang, Zhaohua Hu, Shaofeng Lin, Lulu Chen, Yingge Li, Changmin Peng, Zhuqing Li, Aihua Sun, Yali Chen, Wenge Zhu, Yu Xue, Yi Yao, Xiangpan Li, Qibin Song, Fuchu He, Weijie Qin, Huadong Pei.
      O-linked β-N-acetyl glucosamine (O-GlcNAc) is attached to proteins under glucose-replete conditions; this posttranslational modification results in molecular and physiological changes that affect cell fate. Here we show that posttranslational modification of serine/arginine-rich protein kinase 2 (SRPK2) by O-GlcNAc regulates de novo lipogenesis by regulating pre-mRNA splicing. We found that O-GlcNAc transferase O-GlcNAcylated SRPK2 at a nuclear localization signal (NLS), which triggers binding of SRPK2 to importin α. Consequently, O-GlcNAcylated SRPK2 was imported into the nucleus, where it phosphorylated serine/arginine-rich proteins and promoted splicing of lipogenic pre-mRNAs. We determined that protein nuclear import by O-GlcNAcylation-dependent binding of cargo protein to importin α might be a general mechanism in cells. This work reveals a role of O-GlcNAc in posttranscriptional regulation of de novo lipogenesis, and our findings indicate that importin α is a "reader" of an O-GlcNAcylated NLS.
    Keywords:  O-GlcNAcylation; SRPK2; lipid synthesis; nuclear import
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.009
  8. Trends Microbiol. 2021 Mar 02. pii: S0966-842X(21)00035-4. [Epub ahead of print]
    Microbial Regulation of Host Physiology by Short-chain Fatty Acids.
    Bart van der Hee, Jerry M Wells.
      Our ancestral diet consisted of much more nondigestible fiber than that of many societies today. Thus, from an evolutionary perspective the human genome and its physiological and nutritional requirements are not well aligned to modern dietary habits. Fiber reaching the colon is anaerobically fermented by the gut bacteria, which produce short-chain fatty acids (SCFAs) as metabolic by-products. SCFAs play a role in intestinal homeostasis, helping to explain why changes in the microbiota can contribute to the pathophysiology of human diseases. Recent research has shown that SCFAs can also have effects on tissues and organs beyond the gut, through their circulation in the blood. SCFAs not only signal through binding to cognate G-protein-coupled receptors on endocrine and immune cells in the body but also induce epigenetic changes in the genome through effects on the activity of histone acetylase and histone deacetylase enzymes. Furthermore, epigenetic imprinting likely occurs in utero, highlighting the importance of the maternal diet in early life. Here we review current understanding of how SCFAs impact on human and animal physiology and discuss the potential applications of SCFAs in the prevention and treatment of human diseases.
    DOI:  https://doi.org/10.1016/j.tim.2021.02.001
  9. J Lipid Res. 2021 Feb 26. pii: S0022-2275(21)00038-9. [Epub ahead of print] 100056
    Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells.
    Stacey L Borrego, Johannes Fahrmann, Jue Hou, Da-Wei Lin, Bruce J Tromberg, Oliver Fiehn, Peter Kaiser.
      Methionine is an essential amino acid and critical precursor to the cellular methyl donor S-adenosylmethionine. Unlike non-transformed cells, cancer cells have a unique metabolic requirement for methionine and are unable to proliferate in growth media where methionine is replaced with its metabolic precursor, homocysteine. This metabolic vulnerability is common among cancer cells regardless of tissue origin and is known as "methionine dependence", "methionine stress sensitivity", or the Hoffman effect. The response of lipids to methionine stress, however, is not well-understood. Using mass spectroscopy, label-free vibrational microscopy, and next-generation sequencing, we characterize the response of lipids to methionine stress in the triple-negative breast cancer cell line MDA-MB-468 and its methionine stress insensitive derivative, MDA-MB-468res-R8. Lipidome analysis identified an immediate, global decrease in lipid abundances with the exception of triglycerides and an increase in lipid droplets in response to methionine stress specifically in MDA-MB-468 cells. Furthermore, specific gene expression changes were observed as a secondary response to methionine stress in MDA-MB-468, resulting in a downregulation of fatty acid metabolic genes and an upregulation of genes in the unfolded protein response pathway. We conclude that the extensive changes in lipid abundance during methionine stress is a direct consequence of the modified metabolic profile previously described in methionine stress sensitive cells. The changes in lipid abundance likely results in changes in membrane composition inducing the unfolded protein response we observe.
    Keywords:  Cancer metabolism; Fatty acid metabolism; Homocysteine; Lipid droplets; Lipid metabolism; Methionine; Methionine stress; Phospholipids; Triglycerides
    DOI:  https://doi.org/10.1016/j.jlr.2021.100056
  10. Nat Commun. 2021 Mar 05. 12(1): 1455
    Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
    Man Hsin Hung, Joo Sang Lee, Chi Ma, Laurence P Diggs, Sophia Heinrich, Ching Wen Chang, Lichun Ma, Marshonna Forgues, Anuradha Budhu, Jittiporn Chaisaingmongkol, Mathuros Ruchirawat, Eytan Ruppin, Tim F Greten, Xin Wei Wang.
      T-cell exhaustion denotes a hypofunctional state of T lymphocytes commonly found in cancer, but how tumor cells drive T-cell exhaustion remains elusive. Here, we find T-cell exhaustion linked to overall survival in 675 hepatocellular carcinoma (HCC) patients with diverse ethnicities and etiologies. Integrative omics analyses uncover oncogenic reprograming of HCC methionine recycling with elevated 5-methylthioadenosine (MTA) and S-adenosylmethionine (SAM) to be tightly linked to T-cell exhaustion. SAM and MTA induce T-cell dysfunction in vitro. Moreover, CRISPR-Cas9-mediated deletion of MAT2A, a key SAM producing enzyme, results in an inhibition of T-cell dysfunction and HCC growth in mice. Thus, reprogramming of tumor methionine metabolism may be a viable therapeutic strategy to improve HCC immunity.
    DOI:  https://doi.org/10.1038/s41467-021-21804-1
  11. Oncogene. 2021 Mar 05.
    PSPH promotes melanoma growth and metastasis by metabolic deregulation-mediated transcriptional activation of NR4A1.
    Vipin Rawat, Parmanand Malvi, Deborah Della Manna, Eddy S Yang, Suresh Bugide, Xuchen Zhang, Romi Gupta, Narendra Wajapeyee.
      Metabolic deregulation, a hallmark of cancer, fuels cancer cell growth and metastasis. Here, we show that phosphoserine phosphatase (PSPH), an enzyme of the serine metabolism pathway, is upregulated in patient-derived melanoma samples. PSPH knockdown using short hairpin RNAs (shRNAs) blocks melanoma tumor growth and metastasis in both cell culture and mice. To elucidate the mechanism underlying PSPH action, we evaluated PSPH shRNA-expressing melanoma cells using global metabolomics and targeted mRNA expression profiling. Metabolomics analysis showed an increase in 2-hydroxyglutarate (2-HG) levels in PSPH knockdown cells. 2-HG inhibits the TET family of DNA demethylases and the Jumonji family of histone demethylases (KDM and JMJD), which is known to impact gene expression. Consistent with these data, PSPH knockdown in melanoma cells showed reduced DNA 5-hydroxymethylcytosine (5hmC) and increased histone H3K4me3 modifications. 2-HG treatment also inhibited melanoma growth. The nCounter PanCancer Pathways Panel-based mRNA expression profiling revealed attenuation of a number of cancer-promoting pathways upon PSPH knockdown. In particular, PSPH was necessary for nuclear receptor NR4A1 expression. Ectopic NR4A1 expression partly rescued the growth of melanoma cells expressing PSPH shRNA. Collectively, these results link PSPH to the facilitation of melanoma growth and metastasis through suppression of 2-HG and thus activation of pro-oncogenic gene expression.
    DOI:  https://doi.org/10.1038/s41388-021-01683-y
  12. Animals (Basel). 2021 Feb 19. pii: 544. [Epub ahead of print]11(2):
    How Does Protein Nutrition Affect the Epigenetic Changes in Pig? A Review.
    Pablo Jesús Marín-García, Lola Llobat.
      Epigenetic changes regulate gene expression and depend of external factors, such as environment and nutrition. In pigs, several studies on protein nutrition have been performed to improve productive and reproductive traits. Indeed, these studies aimed not only to determine broad protein requirements but also pigs' essential amino acids requirements. Moreover, recent studies tried to determine these nutritional requirements for each individual, which is known as protein precision nutrition. However, nutritional changes could affect different epigenetic mechanisms, modifying metabolic pathways both in a given individual and its offspring. Modifications in protein nutrition, such as change in the amino acid profile, increase or decrease in protein levels, or the addition of metabolites that condition protein requirements, could affect the regulation of some genes, such as myostatin, insulin growth factor, or genes controlling cholesterol and glucose metabolism pathways. This review summarizes the impact of most common protein nutritional strategies on epigenetic changes and describes their effects on regulation of gene expression in pigs. In a context where animal nutrition is shifting towards precision protein nutrition (PPN), further studies evaluating the effects of PPN on animal epigenetic are necessary.
    Keywords:  amino acids; epigenetic changes; ideal protein; lysine; methionine; methyl group donors; pig; precision nutrition
    DOI:  https://doi.org/10.3390/ani11020544
  13. Bio Protoc. 2020 Sep 20. 10(18): e3765
    Immunoprecipitation of Acetyl-lysine And Western Blotting of Long-chain acyl-CoA Dehydrogenases and Beta-hydroxyacyl-CoA Dehydrogenase in Palmitic Acid Treated Human Renal Tubular Epithelial Cells.
    Tingting Lv, Suwei Zhu, Yuan Ma, Hong Feng, Qiang Wan.
      As one of the main energy metabolism organs, kidney has been proved to have high energy requirements and are more inclined to fatty acid metabolism as the main energy source. Long-chain acyl-CoA dehydrogenases (LCAD) and beta-hydroxyacyl-CoA dehydrogenase (beta-HAD), key enzymes involved in fatty acid oxidation, has been identified as the substrate of acetyltransferase GCN5L1 and deacetylase Sirt3. Acetylation levels of LCAD and beta-HAD regulate its enzymes activity and thus affect fatty acid oxidation rate. Moreover, immunoprecipitation is a key assay for the detection of LCAD and beta-HAD acetylation levels. Here we describe a protocol of immunoprecipitation of acetyl-lysine and western blotting of LCAD and beta-HAD in palmitic acid treated HK-2 cells (human renal tubular epithelial cells). The scheme provides the readers with clear steps so that this method could be applied to detect the acetylation level of various proteins.
    Keywords:  Acetylation; Beta-HAD; HK-2 cells; Immunoprecipitation; LCAD; Palmitic acid (PA)
    DOI:  https://doi.org/10.21769/BioProtoc.3765
  14. Parasitol Res. 2021 Mar 03.
    Lysine crotonylation is widespread on proteins of diverse functions and localizations in Toxoplasma gondii.
    Fa-Cai Li, Lan-Bi Nie, Hany M Elsheikha, Fang-Yuan Yin, Xing-Quan Zhu.
      Lysine crotonylation (Kcr) is an evolutionally conserved post-translational modification (PTM) on histone proteins. However, information about Kcr and its involvement in the biology and metabolism of Toxoplasma gondii is limited. In the present study, a global Kcr proteome analysis using LC-MS/MS in combination with immune-affinity method was performed. A total of 12,152 Kcr sites distributed over 2719 crotonylated proteins were identified. Consistent with lysine acetylation and succinylation in Apicomplexa, Kcr was associated with various metabolic pathways, including carbon metabolism, pyrimidine metabolism, glycolysis, gluconeogenesis, and proteasome. Markedly, many stage-specific proteins, histones, and histone-modifying enzymes related to the stage transition were found to have Kcr sites, suggesting a potential involvement of Kcr in the parasite stage transformation. Most components of the apical secretory organelles were identified as crotonylated proteins which were associated with the attachment, invasion, and replication of T. gondii. These results expanded our understanding of Kcr proteome and proposed new hypotheses for further research of the Kcr roles in the pathobiology of T. gondii infection.
    Keywords:  Lysine crotonylation; Posttranslational modification (PTM); Tachyzoite; Toxoplasma gondii
    DOI:  https://doi.org/10.1007/s00436-021-07057-3
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